For a general overview of carrot, see the Carrot Facts Page
| Name | Description |
|---|---|
A published collection of 55,386 SSR primer pairs. GMATA (Genome-wide Microsatellite Analyzing Tool Package) software was utilized for mining the genome assembly https://www.ncbi.nlm.nih.gov/nuccore/LNRQ00000000 for SSRs and designing primers from the flanking sequences. Applied microsatellite search parameters for mononucleotide repeats were: Min. length (nt): 1, Max. length (nt): 1, Min. repeat-times: 10. Search parameters for tandem repeats of two to six nucleotides were: Min. length (nt): 2, Max. length (nt): 6, Min. repeat-times: 5. Parameters for marker primer design were: Min. amplicon size: 100 bp, Max. amplicon size: 300 bp, Optimal annealing Tm: 60 °C, Flanking sequence length: 400 bp, Max. template length (the genome is partitioned to individual segments for each SSR): 2000 bp. The high-throughput marker design process produced a total of 55,386 primer pairs that are predicted to amplify 67,279 SSR loci, corresponding to an overall average density of 5.38 kilobases (kb)/marker interval. Marker loci were evenly distributed across the nine carrot chromosomes with marker densities ranging from 5.22 kb/marker interval (chromosome 6) to 5.47 kb/marker interval (chromosome 3). The start and end positions of the SSR loci in the chromosome sequences, the repeat motifs, number of repeats, flanking primer sequences and annealing temperatures can be accessed at https://figshare.com/articles/Marker_data/8593337/2 as ‘SSR Locus Information and Primer Data.xls’. Data from this analysis can be viewed in JBrowse here. | |
Carrot root tissue was collected from three yellow (yyY2Y2) and three orange (yyy2y2) pigmented biological replicates, plants from the progenitor F2 population of population 74,146, at 40 (time point one) and 80 (time point two) days after planting (DAP). Two time points were sampled to detect potential variation in expression across development. Time point one corresponds to the onset of visual detection of carotenoid accumulation in the storage root, and time point two corresponds to the onset of the plateau in carotenoid accumulation. Total RNA was extracted from storage root tissue using the TRIzol Plus RNA Purification Kit (Life Technologies, Carlsbad, CA) in accordance with the manufacturer’s protocol. Contaminating DNA was removed with the TurboDNA-free kit (Life Technologies, Carlsbad, CA). RNA quantity and integrity was confirmed with an Experion RNA StdSens Analysis kit (Bio-Rad, Hercules, CA). All samples had RQI values >8.0. For each sample, a 133-nt insert size paired-end library was prepared at the Biotechnology Center, UW-Madison. Libraries were sequenced on Illumina HiSeq2000 lanes using 2 × 100 nt reads. Reads were filtered with Trimmomatic version 0.32 with adapter trimming and using a sliding window of length ≥50 and quality ≥28, i.e., “ILLUMINACLIP:adapterfna:2:40:15 LEADING:28 TRAILING:28 MINLEN:50 SLIDINGWINDOW:10:28.” Short reads from each replicate were independently mapped against the carrot genome sequence using Bowtie2 (Langmead and Salzberg 2012) and Tophat2 (Kim et al. 2013) (Table S4 in 10.1534/g3.117.043067 Supplementary File S1.xlsx). Differential expression was analyzed with Cufflinks (Trapnell et al. 2012). The three technical replicates for each sample were merged during analysis. Expression data from this analysis is derived from the cufflinks "cds_exp.diff" file. | |
A de novo assembly of carrot ESTs from four genetic backgrounds using the Illumina platform and Sanger sequencing. Normalized cDNA libraries were constructed from four sources: two orange unrelated inbred lines of European origin, B493 and B6274 with Imperator and Nantes root shapes, respectively; a purple/yellow inbred line B7262 derived from an intercross between purple Turkish and orange Danvers (European) carrots; and a pool of F₄ RILs derived from a cross between B493 and QAL, a wild carrot from North America. These pooled F₄'s are referred to as B493 × QAL and were derived from a single B493 × QAL F₁ plant. Therefore at most two haplotypes are represented among these transcripts. A total of 18,044 high quality Sanger sequences were obtained from the B493 library to generate a total of 8,221,411 nt with an average length of 456 nt. These sequences are deposited in GenBank under accession numbers JG753039 through JG771082. The three other libraries, B6274, B7262 and B493 × QAL were sequenced with Illumina GAII platform with 61 cycles to yield from 34 M to 39 M usable reads of 41 nt or longer for each genotype. These reads are available in the NCBI SRA archive under accession number SRA035376. A CAP3 assembly of B493 Sanger sequences produced 4,044 contigs plus 3,241 singletons (Additional file 1, Table S1). A multiple step assembly strategy was used to produce a de novo assembly of the three Illumina sequence sets. For each genotype two separate assemblies were produced using either Velvet combined with CAP3, or ABySS. The Velvet+CAP3 assembly gave 31,337, 34,218, and 39,901 contigs for B6274, B7262, and B493 × QAL, respectively. The number of contigs produced by ABySS assembly was higher, ranging from 133,933 in B6274 to 193 844 for B493 × QAL. To combine the four sequences sources (B493, B493 × QAL, B6272 and B7262), a combined CAP3 assembly was created of contigs ≥100 nt. This cut off was selected based on annotation frequency vs. contig length. The resulting sequence assembly produced 57,840 contigs plus 911 Sanger singletons with a total sequence length of about 45 Mb. The average length of the contigs and singletons was 768.2 nt and the N50 (the contig lengths for which 50% of the sequence in an assembly is in contig of this size or larger) was 1378 nt. Out of the 58,751 contigs and singletons, 6,912 (11.7%) contained B493 Sanger sequences. Among the Illumina-sequenced genotypes, B7262 sequences were most common in contigs, represented in 50,057 contigs (85.2%). Comparing Illumina-sequenced transcriptomes, a total of 19,762 contigs (38.1%) contained reads from only two genotypes, with 18.3% of the contigs having reads from B493 × QAL and B7262, 9.4% from B493 × QAL and B6274, and 10.4% from B7262 and B6274. More than 50% of the assembled contigs contained sequences from all three genotypes. B7262 had the highest number of genotype specific contigs (1,494, 2.9%), and B6274 had the lowest with 1,017 (2.0%) genotype specific genes. The sequences available for download are these 58,751 sequences from "Additional file 2" from the publication. | |
Coordinates of 4028 DcSto insertions belonging to 14 families were compared to coordinates of ca. 32 thousand genes annotated in the carrot reference DH1 genome assembly (Iorizzo et al., 2016; NCBI accession LNRQ01000000). 609 gene-associated DcSto insertion sites localized in introns were identified, of which 209 were manually selected for development of ILP markers. The criteria for initial selection were as followed: insertion sites were (1) free from any other annotated repetitive sequences, (2) present in introns not longer than 3.7 Kb, and (3) evenly distributed over each chromosome. Primer3 (Untergasser et al., 2012) and Primer-BLAST (Ye et al., 2012) were used to design PCR primer pairs anchored in exons flanking introns harboring the selected DcSto insertions. Primer pairs were designed to amplify fragments in a 400–3,700-bp range. The optimal annealing temperature was set to 58°C; and the size and GC content ranged from 18 to 23 bases and 40 to 60%, respectively. Primer pairs from supplementary table 2 were located on the carrot genome by in silico PCR. Data from this analysis can be viewed in JBrowse here. | |
L8708 × Z020 Linkage Map Variants The F2 population, L8708 × Z020, was identified from prior field screening as segregating for plant height, shoot biomass, and root storage shape and color. This population was derived from a cross between L8708, an orange inbred line with a medium-long storage root and compact shoots, and Z020, a yellow, cultivated landrace from Uzbekistan with a short, blunt-tipped storage root and broad, prostrate leaves. A single F1 plant was selected from this cross and selfed to produce the F2 population used for mapping in this study. Variants were obtained using genotyping-by-sequencing (GBS). Genomic DNA was digested with ApeK1, barcoded, and pooled for sequencing with 85–95 pooled samples per Illumina HiSeq 2000 lane. Samples were sequenced using single end, 100 nt reads and v3 SBS reagents (Illumina, San Diego, CA, United States). SNPs were called using the TASSEL-GBS pipeline version 5.2.31. Filtering was conducted in VCFtools version 0.1.14 with the following parameters: a minimum minor allele frequency of 0.1 and maximum missing data of 10% for both genotype and marker. The filtered vcf file contains 116,030 variants. Only the 640 mapped markers have PASS status in the vcf file. This file can be downloaded from the link below. The linkage map from this publication can be viewed at L8708×Z020 Data from this analysis can be viewed in JBrowse here. | |
Mobile elements in the genome assembly were identified at both the DNA and protein level. RepeatMasker v3.2.9 (http://www.repeatmasker.org/) was applied to screen the genome assembly for low complexity DNA sequences and interspersed repeated elements using a custom library (a combination of Repbase v16.02 and plant repeat database). RepeatProteinMask (an extension of RepeatMasker) was used to perform RMBlast against the ME protein database to find known repeat sequences at the protein level. Ab initio prediction program RepeatModeler version 1.0.4 (http://www.repeatmasker.org/RepeatModeler/) was employed to build the de novo repeat library from the assembled genome, refined by removing the contaminated sequences possibly derived from bacterial and redundant duplicated sequences in the library. Using this library as a database, RepeatMasker was implemented to identify and classify homologous repeat elements in the genome. In addition, LTR_FINDER version 1.1.0.5 was used to search the whole genome for the characteristic structure of the full-length long terminal repeat (LTR) retrotransposons. Subsequently, a custom program was used to merge all the predictions and generate a combined repetitive sequence annotation to mask the carrot genome. ME accounted for 44.9% (190 Mb) of the assembled carrot genome. This value is larger than those observed in other sequenced genomes of similar size, for example, grape (41.4%, for 487 Mb) and melon (20%, for 375 Mb). With 57.4 Mb, the fraction of class II transposable elements in the carrot genome is higher than in most other plant genomes including rice (48 Mb). A large fraction of MEs are of relatively recent origin, with a sequence divergence rate of less than 10%. Data from this analysis can be viewed in JBrowse here. | |
Tandem repeats were detected using Tandem Repeats Finder v4.07b. The annotation file used for JBrowse can be downloaded from the link below. Data from this analysis can be viewed in JBrowse here. | |
This analysis represents one step of the whole genome assembly process, the gap fill process. This is described in section 1.3.1 of the Supplementary Note of the referenced publication. Gaps were filled using GapCloser for SOAPdenovo which uses the paired-end information to retrieve the read pairs in which one end is mapped to the unique contig and the other is located within a gap region. These read pairs are then used to perform a local assembly to fill gaps. The result was designated carrot assembly v1.0, which resulted in 4,182 scaffolds covering 418 Mb with an N50 (50% of the genome is in fragments of this length or longer) of 8.073×105nt and 3,914 contigs covering 5.4×106nt with an N50 of 1.8×103nt. Scaftigs covered 3.906×105nt with an N50 of 3.11×104nt. Data from this analysis can be viewed in JBrowse here. | |
An orange, doubled-haploid, Nantes-type carrot (DH1) was used for genome sequencing. We used BAC end sequences and a newly developed linkage map with 2,075 markers to correct 135 scaffolds with one or more chimeric regions. The resulting v2.0 assembly spans 421.5 Mb and contains 4,907 scaffolds (N50 of 12.7 Mb), accounting for ∼90% of the estimated genome size of 473 Mb. The scaftig N50 of 31.2 kb is similar to those of other high-quality genome assemblies such as potato and pepper. About 86% (362 Mb) of the assembled genome is included in only 60 superscaffolds anchored to the nine pseudomolecules. The longest superscaffold spans 30.2 Mb, 85% of chromosome 4. There are a few different naming schemes for this assembly. First there is the Phytozome genome ID 388: The authors' sequences and gene predictions were also submitted to Phytozome, and can be accessed at this address: https://phytozome-next.jgi.doe.gov/info/Dcarota_v2_0 LNRQ01: These sequences were then assigned GenBank accession numbers starting at LNRQ01000001.1 which corresponds to DCARv2_Chr1, up to LNRQ01004826.1 which corresponds to an unincorporated contig, DCARv2_C10750146. These reside in bioproject PRJNA268187, which is a subproject of umbrella project PRJNA285926. Assembly GCA_001625215.1: The genome assembly was later defined an accession number GCA_001625215.1 for assembly ASM162521v1 which consists of only the 9 chromosome sequences and the plastid assembly, which have accession numbers from CM004278.1 to CM004286.1 for the chromosomes and CM004358.1 for the plastid. The mitochondrial genome was not included because it is classified as an incomplete sequence. RefSeq: The assembly was then later added to RefSeq, and there another new set of identifiers was defined from NC_030381.1 to NC_030389.1 for the chromosomes, and from NW_016089425.1 to NW_016094239.1 for unincorporated scaffolds and contigs. These reside in bioproject PRJNA326436. Note that NCBI substituted different assembled organellar genomes from different genotypes for the RefSeq records. The NCBI Sequence report lists the correspondences between the various naming methods Link to the LNRQ01000000.1 master record at NCBI Raw Reads: Link to SRA accessions used for the genome assembly This genome is available in the CarrotOmics Blast Search | |
This analysis represents the JBrowse annotation of gaps in the assembled carrot genome sequence. This JBrowse track shows all gaps in the genome assembly consisting of runs of 1 or more 'N's. Gaps of exactly 1000nt are a special case, and represent gaps of undetermined size. Data from this analysis can be viewed in JBrowse here. |
| Name | Description | Units |
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A combination of terpene metabolite profiling, genotyping-by-sequencing (GBS), and genome-wide association study (GWAS) was used in this work to get insights into the genetic control of terpene biosynthesis in carrots and to identify several TPS candidate genes that might be involved in the production of specific monoterpenes. In a panel of 85 carrot cultivars and accessions, metabolite profiling was used to identify 31 terpenoid volatile organic compounds (VOCs) in carrot leaves and roots, and a GBS approach was used to provide dense genome-wide marker coverage (>168,000 SNPs). Based on this data, a total of 30 quantitative trait loci (QTLs) was identified for 15 terpenoid volatiles. Most QTLs were detected for the monoterpene compounds ocimene, sabinene, β-pinene, borneol and bornyl acetate. We identified four genomic regions on three different carrot chromosomes by GWAS which are both associated with high significance (LOD ≥ 5.91) to distinct monoterpenes and to TPS candidate genes, which have been identified by homology-based gene prediction utilizing RNA-seq data. In total, 65 TPS candidate gene models in carrot were identified and assigned to known plant TPS subfamilies with the exception of TPS-d and TPS-h. TPS-b was identified as largest subfamily with 32 TPS candidate genes. | bp | |
Genetic and linkage analysis of marker loci were performed with 4 selfed progenies, derived from single plant (I0/1 lines) of carrot (Daucus carota L. sativus). The analysis of 58 markers included 1 morphological marker, 10 isozyme loci, 14 RFLPs, 28 RAPD markers, and 6 isolated PCR fragments used as RFLP probes. Linkage analysis was carried out with the MAPMAKER program and resulted in the construction of 8 linkage groups containing 55 markers with an average distance of 13.1 cM, 3 marker loci remained unlinked. 24% of the markers deviated significantly from the expected Mendelian ratios (1:2:1 or 3:1) due to gametic or zygotic selection. | cM | |
Genetic and linkage analysis of marker loci were performed with 4 selfed progenies, derived from single plant (I0/1 lines) of carrot (Daucus carota L. sativus). The analysis of 58 markers included 1 morphological marker, 10 isozyme loci, 14 RFLPs, 28 RAPD markers, and 6 isolated PCR fragments used as RFLP probes. Linkage analysis was carried out with the MAPMAKER program and resulted in the construction of 8 linkage groups containing 55 markers with an average distance of 13.1 cM, 3 marker loci remained unlinked. 24% of the markers deviated significantly from the expected Mendelian ratios (1:2:1 or 3:1) due to gametic or zygotic selection. | cM | |
Genetic and linkage analysis of marker loci were performed with 4 selfed progenies, derived from single plant (I0/1 lines) of carrot (Daucus carota L. sativus). The analysis of 58 markers included 1 morphological marker, 10 isozyme loci, 14 RFLPs, 28 RAPD markers, and 6 isolated PCR fragments used as RFLP probes. Linkage analysis was carried out with the MAPMAKER program and resulted in the construction of 8 linkage groups containing 55 markers with an average distance of 13.1 cM, 3 marker loci remained unlinked. 24% of the markers deviated significantly from the expected Mendelian ratios (1:2:1 or 3:1) due to gametic or zygotic selection. | cM | |
Genetic and linkage analysis of marker loci were performed with 4 selfed progenies, derived from single plant (I0/1 lines) of carrot (Daucus carota L. sativus). The analysis of 58 markers included 1 morphological marker, 10 isozyme loci, 14 RFLPs, 28 RAPD markers, and 6 isolated PCR fragments used as RFLP probes. Linkage analysis was carried out with the MAPMAKER program and resulted in the construction of 8 linkage groups containing 55 markers with an average distance of 13.1 cM, 3 marker loci remained unlinked. 24% of the markers deviated significantly from the expected Mendelian ratios (1:2:1 or 3:1) due to gametic or zygotic selection. | cM | |
The mapping population 9304×7262 of 103 F₂ plants was derived from a single F₁ plant of the cross between fertile maintainer inbreds B9304 and YC7262. B9304 had non-purple root phloem, an orange xylem (core) and a high reducing sugar content (p₁p₁y₂y₂RsRs). The roots of YC7262, a full-sib of B7262, had purple phloem, a yellow xylem and a low reducing sugar content (P₁P₁Y₂Y₂rsrs) The map is composed of 99 AFLP, 2 RAPD, 3 SAMPL, and 6 RFLP markers (110 total) and 3 phenotypic loci. The total map length is 534.4 cM in 11 linkage groups. | cM | |
The mapping population 9304×7262 of 103 F₂ plants was derived from a single F₁ plant of the cross between fertile maintainer inbreds B9304 and YC7262. B9304 had non-purple root phloem, an orange xylem (core) and a high reducing sugar content (p₁p₁y₂y₂RsRs). The roots of YC7262, a full-sib of B7262, had purple phloem, a yellow xylem and a low reducing sugar content (P₁P₁Y₂Y₂rsrs) | cM | |
The segregating population employed in the present study was derived from a cross between the M. javanica resistant inbred line ‘Brasilia-1252’ as female parent and the susceptible inbred line ‘B6274B’ as male parent. A single F₁ plant was self-pollinated to produce 442 F₂ individuals that were evaluated for a M. javanica reaction under greenhouse conditions at University of California, Riverside, California. 112 of these individuals were used to construct the linkage map. The map is composed of 10 AFLP markers and 1 phenotypic locus. The total map length is 51.9 cM in 1 linkage group. | cM | |
The segregating population employed in the present study was derived from a cross between the M. javanica resistant inbred line ‘Brasilia-1252’ as female parent and the susceptible inbred line ‘B6274B’ as male parent. A single F₁ plant was self-pollinated to produce 442 F₂ individuals that were evaluated for a M. javanica reaction under greenhouse conditions at University of California, Riverside, California. 412 of these individuals were used to construct the linkage map. The map is composed of 4 RAPD markers and 1 phenotypic locus. The total map length is 6.5 cM in 1 linkage group. | cM | |
The segregating population employed in the present study was derived from a cross between the M. javanica resistant inbred line ‘Brasilia-1252’ as female parent and the susceptible inbred line ‘B6274B’ as male parent. A single F₁ plant was self-pollinated to produce 442 F₂ individuals that were evaluated for a M. javanica reaction under greenhouse conditions at University of California, Riverside, California. 417 of these individuals were used to construct the linkage map. The map is composed of 10 RAPD STS markers and 1 phenotypic locus. The total map length is 14.3 cM in 1 linkage group. Genetic distances between adjacent markers were estimated using Kosambi function. | cM |
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| The organism, Daucus carota subsp. sativus, is a homotypic synonym of organism, Daucus carota var. sativus. |
| Name | Tissue | Treatment | Description |
|---|---|---|---|
| 70796.dOr | storage root | Not set | This biomaterial: 70796.dOr, was created for the analysis: Carrot Genome Assembly V.2 RNAseq population 70796 dOr vs. pOr |
| 70796.pOr | storage root | Not set | This biomaterial: 70796.pOr, was created for the analysis: Carrot Genome Assembly V.2 RNAseq population 70796 dOr vs. pOr |
| 74,146.OrTP1 | storage root | Not set | Dark orange phenotype, yyy₂y₂ genotype |
| 74,146.OrTP2 | storage root | Not set | Dark orange phenotype, yyy₂y₂ genotype |
| 74,146.YTP1 | storage root | Not set | Yellow phenotype, yyY₂Y₂ genotype |
| 74,146.YTP2 | storage root | Not set | Yellow phenotype, yyY₂Y₂ genotype |
| 97837.W | storage root | Not set | This biomaterial: 97837.W, was created for the analysis: Carrot Genome Assembly V.2 RNAseq population 97837 Y vs. W |
| 97837.Y | storage root | Not set | This biomaterial: 97837.Y, was created for the analysis: Carrot Genome Assembly V.2 RNAseq population 97837 Y vs. W |
| SAMN03216637 | leaf | Not set | This biosample is also known by its germplasm accession of DH1, please see this record for more details. |
| SAMN03766317 | leaf | Not set |
| Accession | Accession Type |
|---|---|
| B493A | Generated Germplasm (Breeding Cross) |
| 9304×7262 | Population |
| B1896B | Breeding Research Material |
| 10117 | Population |
| Br1091×HM1 | Population |
| Br1091×HM1F3 | Population |
| SFF×HM2 | Population |
| 2569 | Population |
| 157 Euphytica 1993 | Population |
| 179 Euphytica 1993 | Population |